How to reproduce:
1. Open the attached 'project-1176628.zip' project
2. In the Inspector window select 'Cube' > 'Sphere' and duplicate it (Ctrl+D)

Expected result: an exact duplicate of 'Sphere' is created
Actual result: a modified 'Sphere' object is created

Reproducible with: 2018.4.7f1, 2019.2.2f1, 2019.3.0a12, 2020.0a1
Could not test with: 2017.4.32f1 due to old prefabs system

Notes:
1) Sphere inherits Position offset, Rotation and Scaling from its parent object
2) To reproduce this behavior, the Sphere object has to be a prefab attached to a parent object which is then turned into a prefab
3) Duplicating an already duplicated object will create it in the right position
4) Copying and pasting the object creates it in the right position